From 1cc6646ed138fe298d3e4df9d0b0377c8140ec45 Mon Sep 17 00:00:00 2001 From: Andrew Hoopes Date: Tue, 15 Feb 2022 11:58:37 -0500 Subject: [PATCH] rename segment subfields to subregions --- CMakeLists.txt | 2 +- python/freesurfer/subfields/__init__.py | 4 ---- python/freesurfer/subregions/__init__.py | 4 ++++ .../{subfields => subregions}/brainstem.py | 4 ++-- .../{subfields => subregions}/core.py | 2 +- .../{subfields => subregions}/hippocampus.py | 4 ++-- .../{subfields => subregions}/process.py | 8 ++++---- .../{subfields => subregions}/thalamus.py | 4 ++-- .../{subfields => subregions}/utils.py | 0 subfields/CMakeLists.txt | 3 --- subregions/CMakeLists.txt | 3 +++ .../segment_subregions | 20 +++++++++---------- 12 files changed, 29 insertions(+), 29 deletions(-) delete mode 100644 python/freesurfer/subfields/__init__.py create mode 100644 python/freesurfer/subregions/__init__.py rename python/freesurfer/{subfields => subregions}/brainstem.py (99%) rename python/freesurfer/{subfields => subregions}/core.py (99%) rename python/freesurfer/{subfields => subregions}/hippocampus.py (99%) rename python/freesurfer/{subfields => subregions}/process.py (97%) rename python/freesurfer/{subfields => subregions}/thalamus.py (99%) rename python/freesurfer/{subfields => subregions}/utils.py (100%) delete mode 100644 subfields/CMakeLists.txt create mode 100644 subregions/CMakeLists.txt rename subfields/segment_subfields => subregions/segment_subregions (88%) diff --git a/CMakeLists.txt b/CMakeLists.txt index 1270faaba13..ba9f5da669c 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -659,7 +659,7 @@ if(NOT MINIMAL) qdec_glmfit resurf spline3 - subfields + subregions stat_normalize stim_polar mri_synthseg diff --git a/python/freesurfer/subfields/__init__.py b/python/freesurfer/subfields/__init__.py deleted file mode 100644 index e1a3d46bf1f..00000000000 --- a/python/freesurfer/subfields/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -from freesurfer.subfields.process import structure_names -from freesurfer.subfields.process import run_cross_sectional -from freesurfer.subfields.process import run_longitudinal -from freesurfer.samseg.gemsbindings import setGlobalDefaultNumberOfThreads as set_thread_count diff --git a/python/freesurfer/subregions/__init__.py b/python/freesurfer/subregions/__init__.py new file mode 100644 index 00000000000..37577f1778e --- /dev/null +++ b/python/freesurfer/subregions/__init__.py @@ -0,0 +1,4 @@ +from freesurfer.subregions.process import structure_names +from freesurfer.subregions.process import run_cross_sectional +from freesurfer.subregions.process import run_longitudinal +from freesurfer.samseg.gemsbindings import setGlobalDefaultNumberOfThreads as set_thread_count diff --git a/python/freesurfer/subfields/brainstem.py b/python/freesurfer/subregions/brainstem.py similarity index 99% rename from python/freesurfer/subfields/brainstem.py rename to python/freesurfer/subregions/brainstem.py index e1527a5c81b..c908d433625 100644 --- a/python/freesurfer/subfields/brainstem.py +++ b/python/freesurfer/subregions/brainstem.py @@ -5,8 +5,8 @@ import freesurfer as fs from freesurfer import samseg -from freesurfer.subfields import utils -from freesurfer.subfields.core import MeshModel +from freesurfer.subregions import utils +from freesurfer.subregions.core import MeshModel class BrainstemSubstructures(MeshModel): diff --git a/python/freesurfer/subfields/core.py b/python/freesurfer/subregions/core.py similarity index 99% rename from python/freesurfer/subfields/core.py rename to python/freesurfer/subregions/core.py index 6b5aa30c60f..28b5336e15e 100644 --- a/python/freesurfer/subfields/core.py +++ b/python/freesurfer/subregions/core.py @@ -6,7 +6,7 @@ import freesurfer as fs from freesurfer import samseg -from freesurfer.subfields import utils +from freesurfer.subregions import utils class MeshModel: diff --git a/python/freesurfer/subfields/hippocampus.py b/python/freesurfer/subregions/hippocampus.py similarity index 99% rename from python/freesurfer/subfields/hippocampus.py rename to python/freesurfer/subregions/hippocampus.py index 718244456df..61962985cfe 100644 --- a/python/freesurfer/subfields/hippocampus.py +++ b/python/freesurfer/subregions/hippocampus.py @@ -6,8 +6,8 @@ import freesurfer as fs from freesurfer import samseg -from freesurfer.subfields import utils -from freesurfer.subfields.core import MeshModel +from freesurfer.subregions import utils +from freesurfer.subregions.core import MeshModel class HippoAmygdalaSubfields(MeshModel): diff --git a/python/freesurfer/subfields/process.py b/python/freesurfer/subregions/process.py similarity index 97% rename from python/freesurfer/subfields/process.py rename to python/freesurfer/subregions/process.py index a0a117c7be0..f35e7641433 100644 --- a/python/freesurfer/subfields/process.py +++ b/python/freesurfer/subregions/process.py @@ -3,10 +3,10 @@ import freesurfer as fs from freesurfer import samseg -from freesurfer.subfields import utils -from freesurfer.subfields.thalamus import ThalamicNuclei -from freesurfer.subfields.brainstem import BrainstemSubstructures -from freesurfer.subfields.hippocampus import HippoAmygdalaSubfields +from freesurfer.subregions import utils +from freesurfer.subregions.thalamus import ThalamicNuclei +from freesurfer.subregions.brainstem import BrainstemSubstructures +from freesurfer.subregions.hippocampus import HippoAmygdalaSubfields model_lookup = { diff --git a/python/freesurfer/subfields/thalamus.py b/python/freesurfer/subregions/thalamus.py similarity index 99% rename from python/freesurfer/subfields/thalamus.py rename to python/freesurfer/subregions/thalamus.py index 9a4692f8521..c0980170da6 100644 --- a/python/freesurfer/subfields/thalamus.py +++ b/python/freesurfer/subregions/thalamus.py @@ -5,8 +5,8 @@ import freesurfer as fs from freesurfer import samseg -from freesurfer.subfields import utils -from freesurfer.subfields.core import MeshModel +from freesurfer.subregions import utils +from freesurfer.subregions.core import MeshModel class ThalamicNuclei(MeshModel): diff --git a/python/freesurfer/subfields/utils.py b/python/freesurfer/subregions/utils.py similarity index 100% rename from python/freesurfer/subfields/utils.py rename to python/freesurfer/subregions/utils.py diff --git a/subfields/CMakeLists.txt b/subfields/CMakeLists.txt deleted file mode 100644 index 7eab3380133..00000000000 --- a/subfields/CMakeLists.txt +++ /dev/null @@ -1,3 +0,0 @@ -project(subfields) - -install_pyscript(segment_subfields) diff --git a/subregions/CMakeLists.txt b/subregions/CMakeLists.txt new file mode 100644 index 00000000000..c070d8d1e30 --- /dev/null +++ b/subregions/CMakeLists.txt @@ -0,0 +1,3 @@ +project(subregions) + +install_pyscript(segment_subregions) diff --git a/subfields/segment_subfields b/subregions/segment_subregions similarity index 88% rename from subfields/segment_subfields rename to subregions/segment_subregions index 9282efd298d..7b0d548dad8 100755 --- a/subfields/segment_subfields +++ b/subregions/segment_subregions @@ -2,20 +2,20 @@ import os import freesurfer as fs -from freesurfer import subfields +from freesurfer import subregions description = f''' Cross-sectional and longitudinal segmentation for the following -structures: {", ".join(subfields.structure_names)}. To segment +structures: {", ".join(subregions.structure_names)}. To segment the thalamic nuclei, for example, in a cross-sectional analysis: - segment_subfields thalamus --cross subj + segment_subregions thalamus --cross subj Similarly, for a longitudinal analysis, run: - segment_subfields thalamus --long-base base \\ - --long-tps m00.long.base m24.long.base + segment_subregions thalamus --long-base base \\ + --long-tps m00.long.base m24.long.base where each argument to --long-tps represents a subject timepoint. Output segmentations and computed structure volumes will be @@ -23,7 +23,7 @@ saved to the subject's `mri` subdirectory. ''' parser = fs.utils.ArgumentParser(description=description) -parser.add_argument('structure', help=f'Structure to segment. Options are: {", ".join(subfields.structure_names)}.') +parser.add_argument('structure', help=f'Structure to segment. Options are: {", ".join(subregions.structure_names)}.') parser.add_argument('--cross', help='Subject to segment in cross-sectional analysis.') parser.add_argument('--long-tps', nargs='+', help='Subject timepoints to segment in longitudinal analysis.') parser.add_argument('--long-base', help='Base subject for longitudinal analysis.') @@ -40,7 +40,7 @@ if not fs.fshome(): fs.fatal('FREESURFER_HOME must be set!') # Specify the maximum number of threads the GEMS code will use -subfields.set_thread_count(args.threads) +subregions.set_thread_count(args.threads) # Sanity check on process type if args.cross and (args.long_base or args.long_tps): @@ -92,16 +92,16 @@ for side in sides: 'tempDir': args.temp_dir, }) if args.structure == 'hippo-amygdala': - # Provide some extra data for hippocampal subfields + # Provide some extra data for hippocampal subregions subjParameters['wmParcFileName'] = os.path.join(subjdir, 'mri', 'wmparc.mgz') return subjParameters if args.cross: # Cross-sectional analysis parameters = config_subj_params(args.cross, out_dir=args.out_dir) - subfields.run_cross_sectional(args.structure, parameters) + subregions.run_cross_sectional(args.structure, parameters) else: # Longitudinal analysis baseParameters = config_subj_params(args.long_base, temp_subdir=f'base') tpParameters = [config_subj_params(subj, temp_subdir=f'tp{t:02d}') for t, subj in enumerate(args.long_tps)] - subfields.run_longitudinal(args.structure, baseParameters, tpParameters) + subregions.run_longitudinal(args.structure, baseParameters, tpParameters)